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Team:Newcastle University/Workbench
From 2008.igem.org
Newcastle University
GOLD MEDAL WINNER 2008
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Workbench
Aims:
The proposed Synthetic Biology Workbench (cool name needed) will incorporate the functionality of a biological network modeling and simulation program along with spiffy new algorithms that can be used in modern synthetic biology. This will enable users to finetune the expression of models suitable for their purposes, particularly for such fun activities like iGEM competitions.
From a previously created repository of parts and devices, and using the (gentle) guidance of a set of assembly parameters, users will be able to create, edit and piece together biological networks at varying levels of complexity. Users will be able to piece together parts, adding ribosome binding sites, protein coding regions, terminators, etc. until they have exactly the device they desire.
Once the biological circuit is ready in principle, it can be put into practice. The user will be able to request the optimal biological circuit, composed from BioBricks from the repository.
Objectives:
- get a model
- load from SBML and/or CellML
- create using parts and constraints
- show the model
- network view
- basic parts view. Matt suggested being able to view both strands and flip them around.
- take in conditions for synthetic evolution and send models to the evolutionary algorithm
- output the sequence in a standard format
Outcome
Darwin in Silico (DiS) is the Workbench: the graphical user interface (GUI) for the design of the genetic construct that was engineered into B. subtilis. The evolutionary algorithm, parts repository and the constraints repository work behind the scenes of this interface in the design of the construct.
The user can design a starting point for the genetic construct in the centre window of the GUI by dragging and dropping parts into place. All of the two-component genes are available for this process, as are a large number of promoters, ribosome binding sites, transcription factors and sigma factors. These parts are accessed from the parts repository database and built into a preliminary construct.
The constraints repository aids in the building of this construct by not allowing parts that are not compatible to be dropped in place next to each other. Where parts are compatible with each other, constraint models are incorporated into the construct that define the interactions between these.
The user can also map system inputs to system outputs that can be used by the EA. For example, the user could specify that in the presence of a certain set of quorum sensing peptides that a certain fluorescent protein would light up. The user can then run the EA through DiS, leading to the mutation of the hidden layer and the output of the hidden layer model that fulfils the output requirements the user has set.
All of the different software components were supposed to communicate through DiS. Each team member was responsible for the construction of their component. The outcome of this was a working build, where the evolutionary algorithm could communicate directly with the parts repository, but not with DiS. The components were simply not ready to communicate with each other. Once some more work has been carried out on the various components of the overall project, DiS will be functional.
The opening screen of Darwin in Silico - the Synthetic Biology Workbench. Here, we see the first part of the workflow, the Build, where the initial structure of the proposed circuit is laid out. |
Parts can be dragged from the left pane onto the building area, and connected with different kinds of arrows to indicate different relationships. |
Before moving on to the Behaviour tab, the inputs to the system and the outputs from the circuit are specified by right clicking on the elements. |
In the Behaviour tab, the behaviour of the system is specified by a series of tables. In this image, when the input molecule "CSP" is present in high quantities, both GFP and OFP will also be expressed at high levels. |
Contributors
Lead: Morgan Taschuk
